In recent months, I've upgraded LyX from version 2.3.6 to 2.4.0 RC3 (from the Canonical repos) to 2.4.1 (by compiling from source, as documented here). Along the way I discovered a glitch that apparently occurred during the upgrade from 2.3.6 to 2.4.0.
When you create a new document in LyX, it is initially created using a default template that you can customize. My default template, which I created in a previous millennium, starts all paragraphs flush left and uses what LaTeX calls a "small skip" to provide vertical separation between paragraphs. Yesterday, when I created a new document, I noticed that the first paragraph after a section heading would begin flush left but subsequent paragraphs were indented ... in the LyX GUI. When I compiled to a PDF document, however, every paragraph was flush left. The disconnect between what the GUI showed and what the compiled document contained was, shall we say, a trifle confusing.
Looking at the LaTeX output code (which you can do by selecting View > Code Preview Pane to open a preview of the code to be compiled), I noticed the following LaTeX commands being added to the document.
\setlength{\parskip}{\smallskipamount}
\setlength{\parindent}{0pt}
That reminded me to look at the template's document preamble (Document > Settings... > LaTeX Preamble), and sure enough those commands appeared there. Apparently I added them to the preamble of the default template back when dinosaurs still roamed the earth, and they've been there ever since. In resolving bug #4796, the developers changed how vertical spacing between paragraphs was handled. They now use the parskip LaTeX package. Since, for whatever reason, the template had Document > Settings... > Text Layout > Paragraph Separation set to Indentation: Default, the GUI in the current version indented paragraphs other than those immediately after section breaks. Meanwhile, those two lines in the preamble overrode that when creating the PDF output.
The fix was to create a new default template, which is extremely easy in LyX. You create a new document, customize document settings to your liking, go to Document > Settings... and click the Save as Document Defaults button. In my case, this meant changing Document > Settings... > Text Layout > Paragraph Separation to Vertical Space: Small Skip and deleting the aforementioned lines from the preamble. Now I just need to remember to check and, if necessary, replace the default template after future upgrades.
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